1. Load packages, Import data, Set style

library(tidyverse)
library(ggplot2)
library(plotly)
library(ggpubr)

df_long <- read_csv("data/GMDD_DATA_long_2021-08-17_1214.csv") 
knitr::opts_chunk$set(warning = FALSE, message = FALSE, fig.width = 5, fig.height = 4)

2. Create functions

## this function plots a distribution histogram for each variable ********
plot_score <- function(var, vtitle) {
  df_long$var <- unlist(df_long[, var])
  ggplot(df_long, aes(var)) + 
    geom_bar() +
    theme_minimal() +
    xlab("") +
    ggtitle(vtitle)
}

## this function creates a line graph for each individual ****************
plot_within <- function (data, fun.y, vtitle) {
  data$fun.y <- data[, fun.y]
  data$fun.y <- unlist(data$fun.y)
  ggplot(data, aes(as.numeric(visit), fun.y, group = record_id, color = record_id)) +
    geom_line(alpha = 0.4) +
    theme_classic(base_size = 12) +
    theme(legend.position = "None") +
    labs(title = vtitle)  +
    ylab("") +
    xlab("visit")
}

## this function returns the overall sd for a variable *****************
sd_all <- function(data, var) {
  data$var <- data[, var]
  data$var <- unlist(data$var)
  sd(data$var, na.rm = TRUE)
}

# this function plots the distribution of within-subject sd for a variable, 
# and also plots the overall sd ****************************************
plot_within_sd <- function(data, var, vtitle) {
  sd_var <- sd_all(data, var)
  data$var <- data[, var]
  data$var <- unlist(data$var)
  sd_within_data <- data %>% group_by(record_id) %>% summarize(sd = sd(var, na.rm = TRUE))
  ggplot(sd_within_data, aes(sd)) + geom_density(fill = "lightgrey") +
    geom_vline(data = data, xintercept = sd_var) +
    theme_minimal() +
    ggtitle(vtitle) 
}

3. Visualize the distribution of test scores

Test 18. CGI-S

  • Clinical Global Impression: Severity
  • 1, 3, 5, 7, 9, 11, 13
  • variables: 1

T18v1.

CGI-S

plot_score("cgi_s", "CGI-S")

plot_within(df_long, "cgi_s", "CGI-S - within")

plot_within_sd(df_long, "cgi_s", "CGI-S - within SD")

Test 19. CIRS-G

  • Cumulative Illness Rating Scale - Geriatrics
  • 1, 5, 9, 13
  • variables: 4

T19v1.

CIRS-G: Total

plot_score("cirsg_total_score", "CIRS-G: Total")

plot_within(df_long, "cirsg_total_score", "CIRS-G: Total - within")

plot_within_sd(df_long, "cirsg_total_score", "CIRS-G: Total - within SD")

T19v2.

CIRS-G: Severity Index

plot_score("cirsg_severity_index", "CIRS-G: Severity Index")

plot_within(df_long, "cirsg_severity_index", "CIRS-G: Severity Index - within")

plot_within_sd(df_long, "cirsg_severity_index", "CIRS-G: Severity Index - within SD")

T19v3.

CIRS-G: Level 3 severity

plot_score("cirsg_level3_severity", "CIRS-G: Level 3 severity")

plot_within(df_long, "cirsg_level3_severity", "CIRS-G: Level 3 severity - within")

plot_within_sd(df_long, "cirsg_level3_severity", "CIRS-G: Level 3 severity - within SD")

T19v4.

CIRS-G: Level 4 severity

plot_score("cirsg_level4_severity", "CIRS-G: Level 4 severity")

plot_within(df_long, "cirsg_level4_severity", "CIRS-G: Level 4 severity - within")

plot_within_sd(df_long, "cirsg_level4_severity", "CIRS-G: Level 4 severity - within SD")

Test 20. SRFPC

  • Stroke Risk Factor Prediction Chart
  • 1, 5, 9, 13
  • variables: 1

T20v1.

SRFPC: Total

plot_score("srfpc_total", "SRFPC: Total")

plot_within(df_long, "srfpc_total", "SRFPC: Total - within")

plot_within_sd(df_long, "srfpc_total", "SRFPC: Total - within SD")

Test 21. Social Perception

  • Social Perception
  • 1, 5, 9, 13
  • variables: 3

T21v1.

Social Perception: Affect Naming Total

plot_score("affect_naming_total", "Social Perception: Affect Naming Total")

plot_within(df_long, "affect_naming_total", "Social Perception: Affect Naming Total - within")

plot_within_sd(df_long, "affect_naming_total", "Social Perception: Affect Naming Total - within SD")

T21v2.

Social Perception: Affect Naming Scaled

plot_score("affect_naming_scaled", "Social Perception: Affect Naming Scaled")

plot_within(df_long, "affect_naming_scaled", "Social Perception: Affect Naming Scaled - within")

plot_within_sd(df_long, "affect_naming_scaled", "Social Perception: Affect Naming Scaled - within SD")

T21v3.

Social Perception: Affect Naming - t value

plot_score("affect_naming_t", "Social Perception: Affect Naming - t value")

plot_within(df_long, "affect_naming_t", "Social Perception: Affect Naming - t value - within")

plot_within_sd(df_long, "affect_naming_t", "Social Perception: Affect Naming - t value - within SD")

Test 22. CERAD Neuropsych Battery

  • Social Perception
  • 1, 5, 9, 13
  • variables: 4

T22v1.

CERAD: BNT Boston Naming test Total

plot_score("cerad_bnt_total", "BNT Total")

plot_within(df_long, "cerad_bnt_total", "BNT Total - within")

plot_within_sd(df_long, "cerad_bnt_total", "BNT Total - within SD")

T22v2.

CERAD: Constructional Praxis Total

plot_score("cerad_cp_total", "Constructional Praxis Total")

plot_within(df_long, "cerad_cp_total", "Constructional Praxis Total - within")

plot_within_sd(df_long, "cerad_cp_total", "Constructional Praxis Total - within SD")

T22v3.

CERAD: Word List Recognition Total

plot_score("cerad_wlrec_total", "Word List Recognition Total")

plot_within(df_long, "cerad_wlrec_total", "Word List Recognition Total - within")

plot_within_sd(df_long, "cerad_wlrec_total", "Word List Recognition Total - within SD")

T22v4.

CERAD: Constructional Praxis Recall Total

plot_score("cerad_cpr_total", "Constructional Praxis Recall Total")

plot_within(df_long, "cerad_cpr_total", "Constructional Praxis Recall Total - within")

plot_within_sd(df_long, "cerad_cpr_total", "Constructional Praxis Recall Total - within SD")

Test 23. Go-No Go

  • Go-No Go
  • 1, 5, 9, 13
  • variables: 2

T23v1.

GNG: Conflict

plot_score("gng_conflict", "GNG: Conflict")

plot_within(df_long, "gng_conflict", "GNG: Conflict - within")

plot_within_sd(df_long, "gng_conflict", "GNG: Conflict - within SD")

T23v2.

GNG: Inhibit

plot_score("gng_inhibit", "GNG: Inhibit")

plot_within(df_long, "gng_inhibit", "GNG: Inhibit - within")

plot_within_sd(df_long, "gng_inhibit", "GNG: Inhibit - within SD")

Test 24. PANAS

  • Positive And Negative Affect Schedule
  • all visits
  • variables: 2

T24v1.

PANAS: Positive

plot_score("panas_positive", "PANAS: Positive")

plot_within(df_long, "panas_positive", "PANAS: Positive - within")

plot_within_sd(df_long, "panas_positive", "PANAS: Positive - within SD")

T24v2.

PANAS: Negative

plot_score("panas_negative", "PANAS: Negative")

plot_within(df_long, "panas_negative", "PANAS: Negative - within")

plot_within_sd(df_long, "panas_negative", "PANAS: Negative - within SD")

Test 25. GDS

  • Geriatric Depression Scale
  • all visits
  • variables: 1

T25v1.

GDS: Total

plot_score("gds_total", "GDS: Total")

plot_within(df_long, "gds_total", "GDS: Total - within")

plot_within_sd(df_long, "gds_total", "GDS: Total - within SD")

Test 26. GAD-7

  • Geriatric Depression Scale
  • all visits
  • variables: 2

T26v1.

GAD-7: Total

plot_score("gad_total", "GAD: Total")

plot_within(df_long, "gad_total", "GAD: Total - within")

plot_within_sd(df_long, "gad_total", "GAD: Total - within SD")

T26v2.

GAD-7: Difficulty

plot_score("gad_difficulty", "GAD: Difficulty")

plot_within(df_long, "gad_difficulty", "GAD: Difficulty - within")

plot_within_sd(df_long, "gad_difficulty", "GAD: Difficulty - within SD")

Test 27. WHODAS

  • WHODAS
  • 1, 3, 5, 7, 9, 11, 13
  • variables: 1

T27v1.

WHODAS: sum

plot_score("whodas_s_sum", "WHODAS: Sum")

plot_within(df_long, "whodas_s_sum", "WHODAS: Sum - within")

plot_within_sd(df_long, "whodas_s_sum", "WHODAS: Sum - within SD")

Test 28. FAST-ER

  • FAST-ER
  • all visits
  • variables: 1

T28v1.

FAST-ER: Total

plot_score("faster_total", "FAST-ER: Total")

plot_within(df_long, "faster_total", "FAST-ER: Total - within")

plot_within_sd(df_long, "faster_total", "FAST-ER: Total - within SD")

Test 29. FAS-D

  • Fatigue Associated with Depression
  • all visits
  • variables: 3

T29v1.

FAS-D: Total 

plot_score("fasd_total", "FAS-D: Total")

plot_within(df_long, "fasd_total", "FAS-D: Total - within")

plot_within_sd(df_long, "fasd_total", "FAS-D: Total - within SD")

T29v2.

FAS-D: Total Experience

plot_score("fasd_total_experience", "FAS-D: Total Experience")

plot_within(df_long, "fasd_total_experience", "FAS-D: Total Experience - within")

plot_within_sd(df_long, "fasd_total_experience", "FAS-D: Total Experience - within SD")

T29v3.

FAS-D: Total Impact

plot_score("fasd_total_impact", "FAS-D: Total Impact")

plot_within(df_long, "fasd_total_impact", "FAS-D: Total Impact - within")

plot_within_sd(df_long, "fasd_total_impact", "FAS-D: Total Impact - within SD")

Test 30. Spirituality

  • Spirituality
  • 1, 3, 5, 7, 9, 11, 13
  • variables: 6

T30v1.

Spirituality I: Total

plot_score("spirituality_i_total", "Spirituality I: Total")

plot_within(df_long, "spirituality_i_total", "Spirituality I: Total - within")

plot_within_sd(df_long, "spirituality_i_total", "Spirituality I: Total - within SD")

T30v2.

Spirituality II: Trust

plot_score("spirituality_ii_trust", "Spirituality II: Trust")

plot_within(df_long, "spirituality_ii_trust", "Spirituality II: Trust - within")

plot_within_sd(df_long, "spirituality_ii_trust", "Spirituality II: Trust - within SD")

T30v3.

Spirituality II: Mistrust

plot_score("spirituality_ii_mistrust", "Spirituality II: Mistrust")

plot_within(df_long, "spirituality_ii_mistrust", "Spirituality II: Mistrust - within")

plot_within_sd(df_long, "spirituality_ii_mistrust", "Spirituality II: Mistrust - within SD")

T30v4.

Spirituality III: Total

plot_score("spirituality_iii_total", "Spirituality III: Total")

plot_within(df_long, "spirituality_iii_total", "Spirituality III: Total - within")

plot_within_sd(df_long, "spirituality_iii_total", "Spirituality III: Total - within SD")

T30v5.

Spirituality IV: Positive

plot_score("spitituality_iv_positive", "Spirituality IV: Positive")

plot_within(df_long, "spitituality_iv_positive", "Spirituality IV: Positive - within")

plot_within_sd(df_long, "spitituality_iv_positive", "Spirituality IV: Positive - within SD")

T30v6.

Spirituality IV: Negative

plot_score("spitituality_iv_negative", "Spirituality IV: Negative")

plot_within(df_long, "spitituality_iv_negative", "Spirituality IV: Negative - within")

plot_within_sd(df_long, "spitituality_iv_negative", "Spirituality IV: Negative - within SD")

Test 31. GAS

  • Geriatric Anxiety Scale
  • all visits
  • variables: 4

T31v1.

GAS: Total

plot_score("gas_total", "GAS: Total")

plot_within(df_long, "gas_total", "GAS: Total - within")

plot_within_sd(df_long, "gas_total", "GAS: Total - within SD")

T31v2.

GAS: Somatic

plot_score("gas_somatic", "GAS: Somatic")

plot_within(df_long, "gas_somatic", "GAS: Somatic - within")

plot_within_sd(df_long, "gas_somatic", "GAS: Somatic - within SD")

T31v3.

GAS: Cognitive

plot_score("gas_cognitive", "GAS: Cognitive")

plot_within(df_long, "gas_cognitive", "GAS: Cognitive - within")

plot_within_sd(df_long, "gas_cognitive", "GAS: Cognitive - within SD")

T31v4.

GAS: Affective

plot_score("gas_affective", "GAS: Affective")

plot_within(df_long, "gas_affective", "GAS: Affective - within")

plot_within_sd(df_long, "gas_affective", "GAS: Affective - within SD")

Test 32. PSQI

  • Pittsburgh Sleep Quality Index
  • all visits
  • variables: 1

T32v1.

PSQI: Total

plot_score("psqi_global_score", "PSQI: Total")

plot_within(df_long, "psqi_global_score", "PSQI: Total - within")

plot_within_sd(df_long, "psqi_global_score", "PSQI: Total - within SD")

Test 33. PAI SCZ

  • Personality Assessment Psychosis Subscale
  • 1, 5, 9, 13
  • variables: 4

T33v1.

PAI SCZ: Total (t value)

plot_score("pai_scz_total_t", "PAI SCZ: Total (t value)")

plot_within(df_long, "pai_scz_total_t", "PAI SCZ: Total (t value) - within")

plot_within_sd(df_long, "pai_scz_total_t", "PAI SCZ: Total (t value) - within SD")

T33v2.

PAI SCZ: Psychotic Experiences (t value)

plot_score("pai_scz_psychexp_t", "PAI SCZ: Psychotic Experiences (t value)")

plot_within(df_long, "pai_scz_psychexp_t", "PAI SCZ: Psychotic Experiences (t value) - within")

plot_within_sd(df_long, "pai_scz_psychexp_t", "PAI SCZ: Psychotic Experiences (t value) - within SD")

T33v3.

PAI SCZ: Thought Disorder (t value)

plot_score("pai_scz_thought_t", "PAI SCZ: Thought Disorder (t value)")

plot_within(df_long, "pai_scz_thought_t", "PAI SCZ: Thought Disorder (t value) - within")

plot_within_sd(df_long, "pai_scz_thought_t", "PAI SCZ: Thought Disorder (t value) - within SD")

T33v4.

PAI SCZ: Social Detachment (t value)

plot_score("pai_scz_social_t", "PAI SCZ: Social Detachment (t value)")

plot_within(df_long, "pai_scz_social_t", "PAI SCZ: Social Detachment (t value) - within")

plot_within_sd(df_long, "pai_scz_social_t", "PAI SCZ: Social Detachment (t value) - within SD")

Test 34. MMQ

  • Multi-factorial Memory Questionnaire
  • 1, 5, 9, 13
  • variables: 1

T34v1.

MMQ: Total

plot_score("mmq_total", "MMQ: Total")

plot_within(df_long, "mmq_total", "MMQ: Total - within")

plot_within_sd(df_long, "mmq_total", "MMQ: Total - within SD")